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(v1.2.0.9037) survey on website
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@ -82,7 +82,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9032</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9037</span>
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</span>
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</div>
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@ -177,7 +177,7 @@
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</ul>
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</li>
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<li>
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<a href="../reference/">
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<a href="../reference/index.html">
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<span class="fa fa-book-open"></span>
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Manual
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@ -191,7 +191,7 @@
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</a>
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</li>
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<li>
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<a href="../news/">
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<a href="../news/index.html">
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<span class="far fa far fa-newspaper"></span>
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Changelog
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@ -207,10 +207,10 @@
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</a>
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</li>
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<li>
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<a href="../LICENSE-text.html">
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<span class="fa fa-book"></span>
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<a href="../survey.html">
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<span class="fa fa-clipboard-list"></span>
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Licence
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Survey
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</a>
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</li>
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</ul>
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@ -254,6 +254,7 @@
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<span class='kw'>arrows_colour</span> <span class='kw'>=</span> <span class='st'>"darkblue"</span>,
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<span class='kw'>arrows_size</span> <span class='kw'>=</span> <span class='fl'>0.5</span>,
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<span class='kw'>arrows_textsize</span> <span class='kw'>=</span> <span class='fl'>3</span>,
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<span class='kw'>arrows_textangled</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
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<span class='kw'>arrows_alpha</span> <span class='kw'>=</span> <span class='fl'>0.75</span>,
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<span class='kw'>base_textsize</span> <span class='kw'>=</span> <span class='fl'>10</span>,
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<span class='no'>...</span>
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@ -343,6 +344,10 @@
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<th>arrows_textsize</th>
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<td><p>the size of the text at the end of the arrows</p></td>
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</tr>
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<tr>
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<th>arrows_textangled</th>
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<td><p>a logical whether the text at the end of the arrows should be angled</p></td>
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</tr>
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<tr>
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<th>arrows_alpha</th>
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<td><p>the alpha (transparency) of the arrows and their text</p></td>
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@ -370,7 +375,7 @@
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<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
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<p>The colours for labels and points can be changed by adding another scale layer for colour, like <code>scale_colour_viridis_d()</code> or <code>scale_colour_brewer()</code>.</p>
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<p>The colours for labels and points can be changed by adding another scale layer for colour, like <code><a href='https://ggplot2.tidyverse.org/reference/scale_viridis.html'>scale_colour_viridis_d()</a></code> or <code><a href='https://ggplot2.tidyverse.org/reference/scale_brewer.html'>scale_colour_brewer()</a></code>.</p>
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<h2 class="hasAnchor" id="maturing-lifecycle"><a class="anchor" href="#maturing-lifecycle"></a>Maturing lifecycle</h2>
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@ -382,20 +387,25 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
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<pre class="examples"><span class='co'># `example_isolates` is a dataset available in the AMR package.</span>
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<span class='co'># See ?example_isolates.</span>
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<span class='kw'>if</span> (<span class='fl'>FALSE</span>) {
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<span class='co'># See ?pca for more info about Principal Component Analysis (PCA).</span>
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<span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>dplyr</span>)
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<span class='no'>pca_model</span> <span class='kw'><-</span> <span class='no'>example_isolates</span> <span class='kw'>%>%</span>
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<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='fu'><a href='mo_property.html'>mo_genus</a></span>(<span class='no'>mo</span>) <span class='kw'>==</span> <span class='st'>"Staphylococcus"</span>) <span class='kw'>%>%</span>
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<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='kw'>species</span> <span class='kw'>=</span> <span class='fu'><a href='mo_property.html'>mo_shortname</a></span>(<span class='no'>mo</span>)) <span class='kw'>%>%</span>
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<span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise_all.html'>summarise_if</a></span> (<span class='no'>is.rsi</span>, <span class='no'>resistance</span>) <span class='kw'>%>%</span>
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<span class='fu'><a href='pca.html'>pca</a></span>(<span class='no'>FLC</span>, <span class='no'>AMC</span>, <span class='no'>CXM</span>, <span class='no'>GEN</span>, <span class='no'>TOB</span>, <span class='no'>TMP</span>, <span class='no'>SXT</span>, <span class='no'>CIP</span>, <span class='no'>TEC</span>, <span class='no'>TCY</span>, <span class='no'>ERY</span>)
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<span class='kw'>if</span> (<span class='fu'><a href='https://rdrr.io/r/base/library.html'>require</a></span>(<span class='st'>"dplyr"</span>)) {
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<span class='no'>pca_model</span> <span class='kw'><-</span> <span class='no'>example_isolates</span> <span class='kw'>%>%</span>
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<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='fu'><a href='mo_property.html'>mo_genus</a></span>(<span class='no'>mo</span>) <span class='kw'>==</span> <span class='st'>"Staphylococcus"</span>) <span class='kw'>%>%</span>
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<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='kw'>species</span> <span class='kw'>=</span> <span class='fu'><a href='mo_property.html'>mo_shortname</a></span>(<span class='no'>mo</span>)) <span class='kw'>%>%</span>
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<span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise_all.html'>summarise_if</a></span> (<span class='no'>is.rsi</span>, <span class='no'>resistance</span>) <span class='kw'>%>%</span>
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<span class='fu'><a href='pca.html'>pca</a></span>(<span class='no'>FLC</span>, <span class='no'>AMC</span>, <span class='no'>CXM</span>, <span class='no'>GEN</span>, <span class='no'>TOB</span>, <span class='no'>TMP</span>, <span class='no'>SXT</span>, <span class='no'>CIP</span>, <span class='no'>TEC</span>, <span class='no'>TCY</span>, <span class='no'>ERY</span>)
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<span class='co'># old</span>
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<span class='fu'><a href='https://rdrr.io/r/stats/biplot.html'>biplot</a></span>(<span class='no'>pca_model</span>)
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<span class='co'># old (base R)</span>
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<span class='fu'><a href='https://rdrr.io/r/stats/biplot.html'>biplot</a></span>(<span class='no'>pca_model</span>)
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<span class='co'># new </span>
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<span class='fu'>ggplot_pca</span>(<span class='no'>pca_model</span>)
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<span class='co'># new </span>
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<span class='fu'>ggplot_pca</span>(<span class='no'>pca_model</span>)
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<span class='kw'>if</span> (<span class='fu'><a href='https://rdrr.io/r/base/library.html'>require</a></span>(<span class='st'>"ggplot2"</span>)) {
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<span class='fu'>ggplot_pca</span>(<span class='no'>pca_model</span>) +
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<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/scale_viridis.html'>scale_colour_viridis_d</a></span>() +
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<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/labs.html'>labs</a></span>(<span class='kw'>title</span> <span class='kw'>=</span> <span class='st'>"Title here"</span>)
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}
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}</pre>
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</div>
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<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
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